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Hi, im recently upgrading my speakers since the factory ones were completely destroyed over time..
I have an 2001 325I; US version obviously.

so, I bought a pair of Memphis 15-MC6202 coaxical for the rear deck... no problem there!
then i have a pair of Memphis 15-MCS6 which is a component speaker, it comes with tweeters, so there is a crossover to separate the woofer channel and tweeter channel for output.
this is where my problem starts.
I decided to keep using the factory amp since i wanted all my 10 speakers up and running (by 10 i mean 3 in the front door and 2 on the back each side) . So i cut out the factory tweeters and replaced them with my component tweeter, but since i have a crossover, it feeds through that crossover, that means for the crossover input i have the factory woofers wire. so i let the factory tweeters wire loose for a while... then i decided to be a noob and connect BOTH factory woofer and tweeter wires for my crossover input. well, i got the real detailed sound that i wanted, but it gets nasty when i turn it real up... its like the crossover gets too much frequency and then stops the speakers.
im guessing the problem is my noobness that i plugged both factory tweeters and woofers wires into the crossovers input.

so my question is: should i connect the factory tweeter wires directly to the tweeters? that means i will no longer use my crossover for tweeters since i will be plugging only the woofer wires to the crossover.
or i could just let the factory tweeters wire lose and just use the woofer wire and plug it into crossover and let the crossover separate the signals for woofer and tweeters.
the reason im asking that is "if there is a separate wiring comes from factory amp for each component, that means the sound must be already separated into the amp. so if i only connect the woofer wires to crossover, i should only get low frequencies so my actual high frequencies are wasting."

OR i could just let the woofer wire be for the components speaker system and get a separate tweeters to plug them directly to the factory wiring.

You have to send your aftermarket x over a full range signal in order for it to work as it was intended as designed too. The outputs from your factory amp are already crossed over. The leads going to your woofer/midrange driver are x over at a low range and the leads to your tweeter at a high range. You can not successfully connect both the tweeter And mid leads to the input of your aftermarket x over as you have already found out. It is designed to work with a single input ( channel) that is NOT filtered ( crossed over).
If you are adamant about leaving the factory amp in play then my suggestion to you is this; use the factory tweeter output from the factory amp and connect it directly to your aftermarket tweeter. Then take your mid output from the factory amp and connect it to your aftermarket x over and run your aftermarket mid using its own crossover. You should get the most desirable results this way. You are correct in assuming that using your mid output from your factory amp to the aftermarket x over would result in your components having a gap in the frequency range.

You should be fine. The factory x over point should be well within a reasonable range for the tweets. It's the power output that you would have to worry about as far as damaging the tweeters, and its safe to assume that you aftermarket tweeters are capable of handling more power than your factory ones.